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Two-dimensional gel electrophoresis has been instrumental in the developmentof proteomics. Although it is no longer the exclusive scheme used forproteomics, its unique features make it a still highly valuable tool,especially when multiple quantitative comparisons of samples must be made, andeven for large samples series. However, quantitative proteomics using 2D gelsis critically dependent on the performances of the protein detection methodsused after the electrophoretic separations. This chapter therefore examinescritically the various detection methods (radioactivity, dyes, fluorescence,and silver) as well as the data analysis issues that must be taken into accountwhen quantitative comparative analysis of 2D gels is performed.

The Whereabouts of 2D Gels in Quantitative Proteomics